Little information exists on the molecular and biochemical pathophysiology of subacromial bursitis and rotator cuff disease. We investigated the pattern of expression of cytokines (interleukin [IL]-1beta, IL-1, IL-6, tumor necrosis factor [TNF] alpha, small inducible cytokines), metalloproteases, and cyclooxygenases in the subacromial bursa in patients with rotator cuff disease. Subacromial bursa specimens were prepared for molecular and biochemical analysis in patients undergoing shoulder surgery following an institutional review board-approved protocol. Specimens were analyzed for the presence of cytokines, metalloproteases, and cyclooxygenases by use of microarray for gene expression and immunohistocytochemistry. Microarray analysis for gene expression and immunohistochemistry demonstrated that the expression of several cytokine genes (TNF, IL-1alpha, IL-1beta, and IL-6) was increased in patients with subacromial bursitis compared with control specimens. Furthermore, the expression of metalloproteases (MMP-1 and MMP-9) and cyclooxygenases (COX-1 and COX-2) in the bursitis group was found to be increased as compared with controls. Although further investigation is required, these studies suggest that inflammation of the subacromial bursa does occur in patients with rotator cuff disease. These findings support the role of anti-inflammatory agents in the treatment of subacromial impingement and emphasize the importance of subacromial bursectomy to reduce inflammation in rotator cuff disease.